› 5f8k

X-ray diffraction
2.8Å resolution

Crystal structure of the Bac7(1-16) antimicrobial peptide bound to the Thermus thermophilus 70S ribosome

Released:
DOI: 10.2210/pdb5f8k/pdb
PDB 5f8k coloured by chain and viewed from the front.
PDB 5f8k coloured by chain and viewed from the side.
PDB 5f8k coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
Seefeldt AC, Graf M, Pérébaskine N, Nguyen F, Arenz S, Mardirossian M, Scocchi M, Wilson DN, Innis CA
Nucleic Acids Res 44 2429-38 (2016)
PMID: 26792896

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
Entry contents:
50 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (55 distinct):
50S ribosomal protein L2 Chains: 1D, 2D
Molecule details ›
Chains: 1D, 2D
Length: 275 amino acids
Theoretical weight: 30.4 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 2-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
50S ribosomal protein L3 Chains: 1E, 2E
Molecule details ›
Chains: 1E, 2E
Length: 204 amino acids
Theoretical weight: 22.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-204; Coverage: 99%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chains: 1F, 2F
Molecule details ›
Chains: 1F, 2F
Length: 203 amino acids
Theoretical weight: 22.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 6-208; Coverage: 97%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chains: 1G, 2G
Molecule details ›
Chains: 1G, 2G
Length: 181 amino acids
Theoretical weight: 20.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 2-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chains: 1H, 2H
Molecule details ›
Chains: 1H, 2H
Length: 174 amino acids
Theoretical weight: 18.98 KDa
Source organism: Thermus thermophilus HB8
50S ribosomal protein L9 Chains: 1I, 2I
Molecule details ›
Chains: 1I, 2I
Length: 147 amino acids
Theoretical weight: 16.29 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-147; Coverage: 99%)
Gene names: TTHA0242, rplI
Sequence domains:
50S ribosomal protein L13 Chains: 1N, 2N
Molecule details ›
Chains: 1N, 2N
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chains: 1O, 2O
Molecule details ›
Chains: 1O, 2O
Length: 122 amino acids
Theoretical weight: 13.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
50S ribosomal protein L15 Chains: 1P, 2P
Molecule details ›
Chains: 1P, 2P
Length: 149 amino acids
Theoretical weight: 16.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-149; Coverage: 99%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chains: 1Q, 2Q
Molecule details ›
Chains: 1Q, 2Q
Length: 141 amino acids
Theoretical weight: 15.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
50S ribosomal protein L17 Chains: 1R, 2R
Molecule details ›
Chains: 1R, 2R
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: 1S, 2S
Molecule details ›
Chains: 1S, 2S
Length: 110 amino acids
Theoretical weight: 12.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 3-112; Coverage: 98%)
Gene names: TTHA1676, rplR
50S ribosomal protein L19 Chains: 1T, 2T
Molecule details ›
Chains: 1T, 2T
Length: 131 amino acids
Theoretical weight: 15.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-131; Coverage: 90%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chains: 1U, 2U
Molecule details ›
Chains: 1U, 2U
Length: 116 amino acids
Theoretical weight: 13.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 2-117; Coverage: 98%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: 1V, 2V
Molecule details ›
Chains: 1V, 2V
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
50S ribosomal protein L22 Chains: 1W, 2W
Molecule details ›
Chains: 1W, 2W
Length: 112 amino acids
Theoretical weight: 12.68 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-112; Coverage: 99%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chains: 1X, 2X
Molecule details ›
Chains: 1X, 2X
Length: 95 amino acids
Theoretical weight: 10.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-95; Coverage: 99%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chains: 1Y, 2Y
Molecule details ›
Chains: 1Y, 2Y
Length: 107 amino acids
Theoretical weight: 11.73 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-107; Coverage: 97%)
Gene names: TTHA1681, rplX
Sequence domains:
50S ribosomal protein L25 Chains: 1Z, 2Z
Molecule details ›
Chains: 1Z, 2Z
Length: 203 amino acids
Theoretical weight: 22.85 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-203; Coverage: 99%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
50S ribosomal protein L27 Chains: 10, 20
Molecule details ›
Chains: 10, 20
Length: 77 amino acids
Theoretical weight: 8.69 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 8-84; Coverage: 91%)
Gene names: TTHA1782, rpmA
50S ribosomal protein L28 Chains: 11, 21
Molecule details ›
Chains: 11, 21
Length: 97 amino acids
Theoretical weight: 10.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 2-98; Coverage: 99%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chains: 12, 22
Molecule details ›
Chains: 12, 22
Length: 70 amino acids
Theoretical weight: 8.49 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-70; Coverage: 97%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: 13, 23
Molecule details ›
Chains: 13, 23
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L31 Chains: 14, 24
Molecule details ›
Chains: 14, 24
Length: 69 amino acids
Theoretical weight: 8.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-69; Coverage: 97%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
50S ribosomal protein L32 Chains: 15, 25
Molecule details ›
Chains: 15, 25
Length: 59 amino acids
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chains: 16, 26
Molecule details ›
Chains: 16, 26
Length: 53 amino acids
Theoretical weight: 6.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 2-54; Coverage: 98%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: 17, 27
Molecule details ›
Chains: 17, 27
Length: 48 amino acids
Theoretical weight: 5.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-48; Coverage: 98%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
50S ribosomal protein L35 Chains: 18, 28
Molecule details ›
Chains: 18, 28
Length: 64 amino acids
Theoretical weight: 7.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 2-65; Coverage: 99%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chains: 19, 29
Molecule details ›
Chains: 19, 29
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
30S ribosomal protein S2 Chains: 1b, 2b
Molecule details ›
Chains: 1b, 2b
Length: 231 amino acids
Theoretical weight: 26.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 7-237; Coverage: 90%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chains: 1c, 2c
Molecule details ›
Chains: 1c, 2c
Length: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-207; Coverage: 86%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
30S ribosomal protein S4 Chains: 1d, 2d
Molecule details ›
Chains: 1d, 2d
Length: 208 amino acids
Theoretical weight: 24.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 2-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
30S ribosomal protein S5 Chains: 1e, 2e
Molecule details ›
Chains: 1e, 2e
Length: 148 amino acids
Theoretical weight: 16.14 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-152; Coverage: 91%)
Gene names: TTHA1675, rpsE
Sequence domains:
30S ribosomal protein S6 Chains: 1f, 2f
Molecule details ›
Chains: 1f, 2f
Length: 100 amino acids
Theoretical weight: 11.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-100; Coverage: 99%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
30S ribosomal protein S7 Chains: 1g, 2g
Molecule details ›
Chains: 1g, 2g
Length: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 2-156; Coverage: 99%)
Gene names: TTHA1696, rps7, rpsG
30S ribosomal protein S8 Chains: 1h, 2h
Molecule details ›
Chains: 1h, 2h
Length: 137 amino acids
Theoretical weight: 15.74 KDa
Source organism: Thermus thermophilus HB8
30S ribosomal protein S9 Chains: 1i, 2i
Molecule details ›
Chains: 1i, 2i
Length: 127 amino acids
Theoretical weight: 14.28 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 2-128; Coverage: 99%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 Chains: 1j, 2j
Molecule details ›
Chains: 1j, 2j
Length: 97 amino acids
Theoretical weight: 11.17 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 4-100; Coverage: 92%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: 1k, 2k
Molecule details ›
Chains: 1k, 2k
Length: 114 amino acids
Theoretical weight: 12.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 13-126; Coverage: 88%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: 1l, 2l
Molecule details ›
Chains: 1l, 2l
Length: 122 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-123; Coverage: 92%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: 1m, 2m
Molecule details ›
Chains: 1m, 2m
Length: 116 amino acids
Theoretical weight: 13.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 2-117; Coverage: 92%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 type Z Chains: 1n, 2n
Molecule details ›
Chains: 1n, 2n
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
30S ribosomal protein S15 Chains: 1o, 2o
Molecule details ›
Chains: 1o, 2o
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 2-89; Coverage: 99%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: 1p, 2p
Molecule details ›
Chains: 1p, 2p
Length: 82 amino acids
Theoretical weight: 9.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-82; Coverage: 93%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: 1q, 2q
Molecule details ›
Chains: 1q, 2q
Length: 99 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB8
30S ribosomal protein S18 Chains: 1r, 2r
Molecule details ›
Chains: 1r, 2r
Length: 68 amino acids
Theoretical weight: 7.9 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 20-87; Coverage: 77%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chains: 1s, 2s
Molecule details ›
Chains: 1s, 2s
Length: 83 amino acids
Theoretical weight: 9.46 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 2-84; Coverage: 89%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chains: 1t, 2t
Molecule details ›
Chains: 1t, 2t
Length: 98 amino acids
Theoretical weight: 10.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 6-103; Coverage: 93%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
30S ribosomal protein Thx Chains: 1u, 2u
Molecule details ›
Chains: 1u, 2u
Length: 23 amino acids
Theoretical weight: 2.83 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-24; Coverage: 85%)
Gene names: TTHA1396, rpsU
Cathelicidin-3 Chains: 1y, 2y
Molecule details ›
Chains: 1y, 2y
Length: 16 amino acids
Theoretical weight: 2.08 KDa
Source organism: Bos taurus
Expression system: Not provided
UniProt:
  • Canonical: P19661 (Residues: 131-146; Coverage: 10%)
Gene names: BAC7, CATHL3
23S ribosomal RNA Chains: 1A, 2A
Molecule details ›
Chains: 1A, 2A
Length: 2915 nucleotides
Theoretical weight: 948.01 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: 1B, 2B
Molecule details ›
Chains: 1B, 2B
Length: 120 nucleotides
Theoretical weight: 38.88 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: 1a, 2a
Molecule details ›
Chains: 1a, 2a
Length: 1520 nucleotides
Theoretical weight: 493.56 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
Messenger RNA Chains: 1v, 2v
Molecule details ›
Chains: 1v, 2v
Length: 3 nucleotides
Theoretical weight: 936 Da
tRNAiMet Chains: 1x, 2x
Molecule details ›
Chains: 1x, 2x
Length: 76 nucleotides
Theoretical weight: 24.54 KDa
Sequence domains: tRNA

Ligands and Environments

4 bound ligands:
Ligand MG 2703 x MG
Ligand ZN 12 x ZN
Ligand SF4 2 x SF4
Ligand K 2 x K
15 modified residues:
Ligand PSU 10 x PSU
Ligand 5MU 6 x 5MU
Ligand OMC 2 x OMC
Ligand 5MC 14 x 5MC
Ligand OMG 2 x OMG
Ligand 2MA 2 x 2MA
Ligand OMU 2 x OMU
Ligand 7MG 2 x 7MG
Ligand M2G 2 x M2G
Ligand 2MG 2 x 2MG
Ligand 4OC 2 x 4OC
Ligand UR3 2 x UR3
Ligand MA6 4 x MA6
Ligand 0TD 2 x 0TD
Ligand 4SU 2 x 4SU

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P212121
Unit cell:
a: 209.96Å b: 450.13Å c: 622.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.251 0.249 0.292
Expression system: Not provided

Quick links

Citations

5 review citations

Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design.
Lin et al. (2018)
4 more

1 mention without citation

Non-Lytic Antibacterial Peptides That Translocate Through Bacterial Membranes to Act on Intracellular Targets.
Cardoso et al. (2019)